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<!DOCTYPE html>
<html>
<head>
<link rel="stylesheet" href="assets/css/main.css" />
<title>PALS - Config Generator</title>
</head>
<body>
<div class="container">
<h2 class="center-aligned">Generate Config File for PALS</h2>
<table>
<tr id="common-settings">
<td>
<div class="section">
<table class="table table-striped">
<tr>
<th class="required">General Settings</th>
<td></td>
</tr>
<tr>
<td class="required">
<span id="session_id-1">Identifier</span>
</td>
<td>
<input
type="text"
id="session_id-2"
class="form-control"
name="session_id"
onkeyup="onTextChange(this)"
/>
</td>
</tr>
<tr>
<td class="required">
<span id="input_path-1">File path to image (nifti)</span>
</td>
<td>
<input
type="text"
id="input_path-2"
class="form-control"
name="im_path"
onkeyup="onTextChange(this)"
/>
</td>
</tr>
<tr>
<td class="required">
<span id="input_path-3">File path to mask (nifti)</span>
</td>
<td>
<input
type="text"
id="input_path-4"
class="form-control"
name="les_path"
onkeyup="onTextChange(this)"
/>
</td>
</tr>
<tr>
<td class="required">
<span id="output_path-1">Output directory</span>
</td>
<td>
<input
type="text"
id="output_path-2"
class="form-control"
name="out_dir"
onkeyup="onTextChange(this)"
/>
</td>
</tr>
<tr>
<td><span id="script_run-1">Script Run</span></td>
<td>
<select
id="script_run-2"
class="form-control"
name="run"
value="all"
onchange="onTextChange(this)"
>
<option value="all">all</option>
<option value="bet">bet</option>
<option value="mnireg">mnired</option>
<option value="coreg">coreg</option>
<option value="pals">pals</option>
<option value="skipdone">skipdone</option>
</select>
</td>
</tr>
<tr>
<td class="required">
<span id="input_path-5">Starting Space</span>
</td>
<td>
<select
id="input_path-6"
class="form-control"
name="space"
onchange="onTextChange(this)"
>
<option value="orig">orig</option>
<option value="mni">mni</option>
</select>
</td>
</tr>
<tr>
<td><span id="output_path-3">Results Output Format</span></td>
<td>
<select
id="output_path-4"
class="form-control"
name="out_format"
onchange="onTextChange(this)"
>
<option value="csv">csv</option>
<option value="json">json</option>
</select>
</td>
</tr>
</table>
</div>
</td>
</tr>
<tr id="output-settings">
<td>
<div class="section">
<table class="table table-striped">
<tr>
<th>Path Configuration</th>
<td></td>
</tr>
<tr>
<td class="required">
<span id="output_id-1">ANTs Binaries Folder Path</span>
</td>
<td>
<input
type="text"
id="output_id-2"
class="form-control"
name="ants_path"
onkeyup="onTextChange(this)"
/>
</td>
</tr>
<tr>
<td class="required">
<span id="output_id-3">FSL Binaries Folder Path</span>
</td>
<td>
<input
type="text"
id="output_id-4"
class="form-control"
name="fsl_path"
onkeyup="onTextChange(this)"
/>
</td>
</tr>
<tr>
<td class="required">
<span id="output_id-5">ROIs Folder Path</span>
</td>
<td>
<input
type="text"
id="output_id-6"
class="form-control"
name="rois_path"
onkeyup="onTextChange(this)"
/>
</td>
</tr>
<tr>
<td class="required">
<span id="output_id-7">Template Folder Path</span>
</td>
<td>
<input
type="text"
id="output_id-8"
class="form-control"
name="template_directory"
onkeyup="onTextChange(this)"
/>
</td>
</tr>
</table>
</div>
</td>
</tr>
<tr id="registration">
<td>
<div class="section" id="registration_div">
<table class="table table-striped">
<tr>
<th colspan="2">Configuration for Registration</th>
</tr>
<tr>
<td><span id="reg-1">Registration Method</span></td>
<td>
<select
id="reg-2"
type="text"
class="form-control"
name="reg_method"
onchange="onTextChange(this)"
value="flirt"
>
<option value="flirt">flirt</option>
</select>
</td>
</tr>
<tr>
<td><span id="reg-3">Cost Function</span></td>
<td>
<input
id="reg-4"
type="text"
class="form-control"
value="corratio"
name="reg_costfn"
onkeyup="onTextChange(this)"
/>
</td>
</tr>
<tr>
<td><span id="reg-5">Partial Mask Weighting</span></td>
<td>
<input
id="reg-6"
type="checkbox"
class="form-control"
name="reg_partmask"
onchange="onCheckboxToggle(this)"
/>
</td>
</tr>
<tr>
<td><span id="reg-7">No Mask Weighting</span></td>
<td>
<input
id="reg-8"
type="checkbox"
class="form-control"
name="reg_nomask"
onchange="onCheckboxToggle(this)"
/>
</td>
</tr>
</table>
</div>
</td>
</tr>
<tr id="brain_extraction">
<td>
<div class="section" id="brain_extraction_div">
<table class="table table-striped">
<tr>
<th colspan="2">Configuration for Brain Extraction</th>
</tr>
<tr>
<td><span id="bet-1">BET Vertical Gradient</span></td>
<td>
<input
id="bet-2"
type="number"
value="-0.25"
step="0.05"
class="form-control"
name="bet_g"
onchange="onTextChange(this)"
/>
</td>
</tr>
</table>
</div>
</td>
</tr>
<tr id="qc">
<td>
<div class="section" id="qc_div">
<table class="table table-striped">
<tr>
<th colspan="2">Configuration for QC</th>
</tr>
<tr>
<td><span id="qc-1">GIF Duration</span></td>
<td>
<input
id="qc-2"
type="number"
value="0.5"
step="0.05"
class="form-control"
name="gif_duration"
onchange="onTextChange(this)"
/>
</td>
</tr>
</table>
</div>
</td>
</tr>
<tr>
<td class="center-aligned">
<a href="" id="download-btn" class="btn btn-primary"
>Click here to download the config file</a
>
</td>
</tr>
</table>
</div>
<link
rel="stylesheet"
href="https://stackpath.bootstrapcdn.com/bootstrap/4.1.1/css/bootstrap.min.css"
/>
<link
rel="stylesheet"
href="https://cdnjs.cloudflare.com/ajax/libs/bootstrap-select/1.13.1/css/bootstrap-select.css"
/>
<script src="https://ajax.googleapis.com/ajax/libs/jquery/2.1.1/jquery.min.js"></script>
<script src="https://stackpath.bootstrapcdn.com/bootstrap/4.1.1/js/bootstrap.bundle.min.js"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/bootstrap-select/1.13.1/js/bootstrap-select.min.js"></script>
<script src="assets/js/main.js"></script>
</body>
</html>